Initial pass at a plugin which reduces the extra number of queries triggered by plugins to look for non-existent options in options table. Use this as a starting point for what you are trying to do.

plugin.php

<?php
/**
 * Plugin Name: AnattaDesign Site Optimizer
 * Plugin URI: http://anattadesign.com/
 * Description: This plugin optimizes the site by reducing the extra number of queries triggered by plugins to look for non-existent options in options table
 * Version: 0.1
 * Author: Anatta Design
 * Author URI: http://anattadesign.com/
 */

call_user_func( array( new AnattaOptimizer(),
                       'setup'
                )
);

class AnattaOptimizer {

	function setup() {
		if( is_admin() ) {
			add_action( 'activated_plugin', array( $this, 'force_this_plugin_to_load_first' ) );
		}
		$options = get_option( 'AD_empty_options' );
		if( !$options ) {
			$options = array( 'erp',
			                  'jetpack_id',
			                  'linkssc_enable_links_manager',
			                  'linkssc_default_css',
			                  'wpseo_rss',
			                  'wpseo_internallinks',
			                  'embed_autourls',
			                  'jetpack_holiday_snow_enabled',
			                  'woocommerce_informal_localisation_type',
			                  'woocommerce_ga_id',
			                  'woocommerce_ga_standard_tracking_enabled',
			                  'woocommerce_ga_ecommerce_tracking_enabled',
			                  'woocommerce_google_analytics_settings',
			                  'woocommerce_sharethis',
			                  'woocommerce_sharethis_settings',
			                  'woocommerce_shareyourcart_settings',
			                  'woocommerce_sharedaddy',
			                  'woocommerce_sharedaddy_settings'
			);
			update_option( 'AD_empty_options', $options );
		}
		foreach( $options as $option ) {
			add_filter( 'pre_option_' . $option, '__return_empty_string' );
			add_action( 'add_option_' . $option, array( $this, 'remove_key_from_empty_options_list' ) );
			add_action( 'update_option_' . $option, array( $this, 'updated_option' ) );
			add_action( 'deleted_option' . $option, array( $this, 'delete_option' ) );
			add_action( 'update_option' . $option, array( $this, 'update_option' ), 10, 3 );
			add_action( 'add_option' . $option, array( $this, 'add_option' ), 10, 2 );
		}
	}

	function updated_option() {
		$option = current_filter();
		if( substr( $option, 0, strlen( 'update_option_' ) ) == 'update_option_' ) {
			$option = substr( $option, strlen( 'update_option_' ) );
			$this->remove_key_from_empty_options_list( $option );
		}
	}

	function add_option( $option, $value ) {
		if( '' === $value ) {
			$this->add_key_to_empty_options_list( $option );
		}
	}

	function delete_option( $option ) {
		if( 0 !== strpos( $option, '_' ) ) {
			$this->add_key_to_empty_options_list( $option );
		}
	}

	function update_option( $option, $old_value, $value ) {
		if( '' === $value ) {
			$this->add_key_to_empty_options_list( $option );
		}
	}

	function remove_key_from_empty_options_list( $option ) {
		$options = get_option( 'AD_empty_options' );
		if( !is_array( $options ) ) {
			return;
		}
		$options = array_diff( $options, array( $option ) );
		update_option( 'AD_empty_options', $options );
	}

	function add_key_to_empty_options_list( $option ) {
		$options = get_option( 'AD_empty_options' );
		if( !is_array( $options ) ) {
			$options = array();
		}
		$options[] = $option;
		update_option( 'AD_empty_options', $options );
	}

	function force_this_plugin_to_load_first() {
		$path = str_replace( WP_PLUGIN_DIR . '/', '', __FILE__ );
		if( $plugins = get_option( 'active_plugins' ) ) {
			if( $key = array_search( $path, $plugins ) ) {
				array_splice( $plugins, $key, 1 );
				array_unshift( $plugins, $path );
				update_option( 'active_plugins', $plugins );
			}
		}
	}
}